Structure of PDB 6v93 Chain A

Receptor sequence

>6v93A (length=1259) Species: 559292 (Saccharomyces cerevisiae S288C)

SDYFRIQLNNQDYYMSKPTFLDPSHGESLPLNQFSQVPNIRVFGALPTGH
QVLCHVHGILPYMFIKYDGQITDTSTLRHQRCAQVHKTLEVKIRASFKKL
GNLNFVADVSVVKGIPFYGYHVGWNLFYKISLLNPSCLSRISELIRDGKI
FGKKFEIYESHIPYLLQWTADFNLFGCSWINVDRCYFRSPVLNSILDIDK
LTINDDLQLLLDRFCDFKCNVLSRRDFPRVGNGLIEIDILPQFIKNREKL
QHRDIHHDFLEKLVKPYVSSARDMINELTMQREELSLKEYKEPPETKRHV
SGHQWQSSGEFEAFYKKAQHKTSTGQIPNFENFIDKNQKFSAINTPYEAL
PQLWPRLPQIAGLRYGKRAFVYGEPPFGYQDILNKLEDEGFPKIDYKDPF
FSNPVDLENKPYAYAGKRFEISSTHVSTRIPVQFGGETVSVYNKPTFDMF
SSWKYALKPPTYDAVQKWYNKVPSVHDSLTHLTLEIHANTRSDKIPDPAI
DEVSMIIWCLEEETFPLDLDIAYEGIMIVHKADSTFPTKIQHCINEIPVM
FYESEFEMFEALTDLVLLLDPDILSGFEIHNFSWGYIIERCQKIHQFDIV
RELARVKCSDTWGYAHSSGIMITGRHMINIWRALRSDVNLTQYTIESAAF
NILHKRLPHFSFESLTNMWNAKKSTTELKTVLNYWLSRAQINIQLLRKQD
YIARNIEQARLIGIDFHSVYYRGSQFKVESFLIRICKSESFILLSPGKKD
VRKQKALECVPLVMEPESAFYKSPLIVLDFQSLYPSIMIGYNYCYSTMIG
RVREINLTENNLGVSKFSLPRNILALLKNDVTIAPNGVVYAKTSVRKSTL
SKMLTDILDVRVMIKKTMNEIGDDNTTLKRLLNNKQLALKLLANVTYGYT
SASFSGRMPCSDLADSIVQTGRETLEKAIDIIEKDETWNAKVVYGDTDSL
FVYLPGKTAIEAFSIGHAMAERVTQNNPKPIFLKFEKVYHPSILISKKRY
VGFSYESPSQTLPIFDAKGIETVRRDGIPAQQKIIEKCIRLLFQTKDLSK
IKKYLQNEFFKIQIGKVSAQDFCFAKEVKLGAYKSEKTAPAGAVVVKRRI
NEDHRAEPQYKERIPYLVVKGKQGQLLRERCVSPEEFLEGENLELDSEYY
INKILIPPLDRLFNLIGINVGNWAQEEKRSTTTLSFLIKKLKRQKEYQTL
KTVCRTCSYRYTSDAGIENDHIASKCNSYDCPVFYSRVKAERYLRDNQSV
QREEALISL

3D structure

• PDB: 6v93 Structure and mechanism of B-family DNA polymerase zeta specialized for translesion DNA synthesis.
• Chain: A
• Resolution: 3.1 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	A	D1142 K1194 G1215 R1220 R1221 E1273 Y1279 K1280	D946 K998 G1019 R1024 R1025 E1077 Y1083 K1084
BS02	dna	A	W808 R918 G919 S920 Q921 V956 F1100 S1101 K1193 R1195 L1322 P1353	W612 R722 G723 S724 Q725 V760 F904 S905 K997 R999 L1126 P1157
BS03	SF4	A	P854 C1446 C1449 C1468 C1473 R1479	P658 C1204 C1207 C1226 C1231 R1237
BS04	CA	A	D975 F976 D1144	D779 F780 D948
BS05	CA	A	D975 D1144	D779 D948
BS06	DCP	A	F976 S978 Y980 R1057 K1086 N1090 Y1093 D1144	F780 S782 Y784 R861 K890 N894 Y897 D948

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0046872 metal ion binding
• GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process

• GO:0000724 double-strand break repair via homologous recombination
• GO:0006260 DNA replication
• GO:0006281 DNA repair
• GO:0006974 DNA damage response
• GO:0019985 translesion synthesis
• GO:0042276 error-prone translesion synthesis
• GO:0070987 error-free translesion synthesis

Cellular Component

• GO:0005634 nucleus
• GO:0005739 mitochondrion
• GO:0016035 zeta DNA polymerase complex
• GO:0043231 intracellular membrane-bounded organelle

External links

• PDB: RCSB:6v93, PDBe:6v93, PDBj:6v93
• PDBsum: 6v93
• PubMed: 32807989
• UniProt: P14284|DPOZ_YEAST DNA polymerase zeta catalytic subunit (Gene Name=REV3)